Procedure for generating binaries for Windows 64 bits

Working directory: mykrobe-atlas-cli

1. modify ./mccortex/libs/xxHash/xxhsum.c according to Cyan4973/xxHash#100

2. with cygwin64: (cd ./mccortex && make)

3. with cygwin64: pip install pyinstaller

4. with cygwin64: (cd dist && pyinstaller --workpath='./pyinstaller_build/binary_cache' --distpath='./pyinstaller_build' mykrobe_atlas_pyinstaller.spec)

5. binaries and dependencies: ./dist/pyinstaller_build/mykrobe_atlas

Test dist

for f in /Users/Phelimb/Dropbox/Atlas/test_data/exemplar_seqeuence_data/.fastq do ff=basename $f ./mykrobe_atlas predict --mccortex31_path ./mccortex31 --force non-mycobacterium_saur.fastq tb -1 $f --format json --guess_sequence_method --quiet > ../$ff.json done

for f in /Users/Phelimb/Dropbox/Atlas/test_data/exemplar_seqeuence_data/*.bam do ff=basename $f ./mykrobe_atlas predict --mccortex31_path ./mccortex31 --force non-mycobacterium_saur.fastq tb -1 $f --format json --guess_sequence_method --quiet > ../$ff.json done